I have run the RNASeQC v2.4.2 linux binary on the provided test_data set. A number of fields don't seem to be calculated as expected, i.e. the Unique Rate of Mapped is 1, Duplicate Rate of Mapped is 0, so is Duplicate Rate of Mapped, excluding Globins. Estimated Library Complexity is also 0.
I have run the same version on our bam file, generated with STAR v.2.6.0c, and in the output there are even more fields that have 0 result, such as Base Mismatch, End1 Mapping Rate, End 2 Mapping Rate, rRNA Rate, Estimated Library Complexity. End 1/2 Mismatch rates are "-nan".
Attached here the full metrics outputs from both files. I have run FastQC on our file and am aware that the duplicate and unique rates have different values. I've also tested the complied by our IT version, which gives the same output.
Your feedback on what may be causing these issues is highly appreciated.
Hello,
I have run the RNASeQC v2.4.2 linux binary on the provided test_data set. A number of fields don't seem to be calculated as expected, i.e. the Unique Rate of Mapped is 1, Duplicate Rate of Mapped is 0, so is Duplicate Rate of Mapped, excluding Globins. Estimated Library Complexity is also 0.
I have run the same version on our bam file, generated with STAR v.2.6.0c, and in the output there are even more fields that have 0 result, such as Base Mismatch, End1 Mapping Rate, End 2 Mapping Rate, rRNA Rate, Estimated Library Complexity. End 1/2 Mismatch rates are "-nan".
Attached here the full metrics outputs from both files. I have run FastQC on our file and am aware that the duplicate and unique rates have different values. I've also tested the complied by our IT version, which gives the same output.
Your feedback on what may be causing these issues is highly appreciated.
downsampled.bam.metrics.xlsx CustomSTAR2.6.0c.Aligned.sortedByCoord.out.bam.metrics.xlsx